Modified lipopolysaccharide glycoform and method of use

ABSTRACT

The present disclosure generally relates to genetic engineering of bacteria. More particularly, the present disclosure describes genetic engineering of  E. coli  to create mutant O-antigen ligase, as well as novel lipopolysaccharide molecules resulting from that genetic engineering. Methods for using those novel molecules are also described.

CROSS-REFERENCE TO PRIOR FILED APPLICATIONS

This application is a divisional application of U.S. patent application Ser. No. 15/586,781, filed May 4, 2017, now U.S. Pat. No. 10,525,126, which is a divisional application of U.S. patent application Ser. No. 14/707,718, filed May 8, 2015, now U.S. Pat. No. 9,677,052. This application also claims the benefit of U.S. Provisional Application No. 61/991,116, filed May 9, 2014, and U.S. Provisional Application No. 62/098,014, filed Dec. 30, 2014, which are incorporated herein in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under Grant No. GM034821 awarded by the National Institutes of Health and Grant No. AI081059 awarded by the National Institutes of Health. The government has certain rights in this invention.

BACKGROUND OF THE INVENTION

A peptidoglycan (PG) cell wall is an essential extracytoplasmic feature of most bacteria (Singer et al., 1989); this essentiality has made its biogenesis a fruitful target for antibiotics, including vancomycin and penicillin. The cell wall is directly exposed to the extracellular milieu in Gram-positive bacteria, but is shielded in Escherichia coli (E. coli) and other Gram-negative species by a highly selective permeability barrier formed by the outer membrane (OM). The OM prevents influx of antibiotics, such as vancomycin, restricting their access to intracellular targets (Eggert et al., 2001; Ruiz et al., 2005).

Lipopolysaccharide (LPS) forms the surface-exposed outer leaflet of the OM and is key to the barrier function (Osborn et al., 1972; Kamio and Nikaido, 1976; Nikaido, 2003). LPS is a glycolipid consisting of a ‘lipid A’ anchor within the bilayer, and a set of covalently attached distal ‘core’ saccharides (Raetz and Whitfield, 2002). LPS is made at the cytosolic leaflet of the inner membrane (IM) before being flipped to the periplasmic leaflet (Zhou et al., 1998). A transenvelope complex of seven lipopolysaccharide transport proteins (LptABCDEFG) delivers LPS from the IM to the OM (Ruiz et al., 2009; Chng, Gronenberg, et al., 2010). A sub-complex of the β-barrel LptD and lipoprotein LptE resides within the OM and accomplishes the final step of inserting LPS into the outer leaflet (Chng, Ruiz, et al., 2010).

LPS and PG are both potent activators of immune responses via distinct stimulatory mechanisms. However, LPS is inherently toxic to humans and animals due to hyper-activation of inflammatory immune responses. Detoxification can eliminate some or all of the endotoxicity, but the less toxic variants generally also have reduced immunostimulatory properties. LPS-stimulated immune responses can be synergistically increased by co-stimulation with PG added into a mixture (Fritz et al., 2005). Therefore, this synergy is likely to be improved by direct coupling of LPS and PG into a single molecule that allows both activators to stimulate their associated pathways. A detoxified LPS-PG molecule will likely retain more desirable immunostimulatory properties in comparison to detoxified LPS alone.

BRIEF SUMMARY OF THE INVENTION

Mutant O-antigen ligases are disclosed. It includes isolated proteins that have the amino acid sequence SEQ ID NO: 1, or isolated proteins having at least 90% sequence identity to SEQ ID NO: 2 and having an amino acid substitution of phenylalanine to serine at the phenylalanine homologous to position 332 of SEQ ID NO: 2. A vaccine adjuvant may also be produced from a lipopolysaccharide or a lipopolysaccharide derivative isolated from a mutant O-antigen ligase. A polynucleotide may also encode a mutant O-antigen ligase.

A LPS glycoform modified with peptidoglycan cell wall fragments is also disclosed. The LPS glycoform may be adapted to display antibiotic-specific binding sites at a cell surface, of which vancomycin is one such antibiotic. The LPS glycoform may be able to activate receptors or signaling pathways within the human body, including TRL4/MD2 NOD1, and NOD2 receptors, and the TRIF/TRAM pathways.

A bacterium that expresses a LPS glycoform is also disclosed. The bacterium may include a gene encoding a mutant O-antigen ligase.

A method for creating an LPS molecule is also disclosed. An E. coli strain is provided that expresses a mutant O-antigen ligase, it is placed in conditions allowing it to grow, and then the LPS molecule is isolated. The LPS molecule may be isolated by separating the molecules based on at least one of the group consisting of size, chemical composition, and affinity for a particular binding agent.

A method for generating a LPS* derivative molecule is also disclosed. An E. coli strain is provided that expresses a LPS derivative molecule having reduced endotoxicity, modifying the E. coli strain by creating a mutant O-antigen ligase, and placing it in conditions allowing it to grow and produce the LPS* molecule. The LPS* derivative molecule may be isolated at that time. The LPS derivative molecule may be 3-0-deacyl-4′-monophosphoryl lipid A. A vaccine adjuvant may also be created, comprising the LPS* derivative molecule.

A modified LPS molecule having at least one non-native sugar and a greater molecular weight as compared to the LPS molecule it is modified from is also disclosed.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 shows analysis of various strains utilizing one aspect of the invention with regards to vancomycin resistance.

FIG. 2 shows analysis of one aspect of the invention with regards to resistance to two alternate antibiotics.

FIGS. 3-4 shows the SDS-PAGE analysis of LPS molecules from various strains.

FIG. 5 shows analysis of various strains utilizing one aspect of the invention with regards to vancomycin resistance.

FIG. 6 shows the structure of Lipid II and schematic of peptidoglycan cleavage by mutanolysin that releases pentapeptide (“A”) and tetrapeptide (“B”) species.

FIG. 7 shows analysis indicating waaL15 isolate LPS treated with mutanolysin cleaves the LPS* modification.

FIG. 8 shows total ion chromatograms for degradation products of LPS and LPS*, and a total ion chromatogram for LPS* degradation.

FIG. 9 shows the equilibrium signal of the reference subtracted SPR binding kinetics at 25° C.

FIG. 10 shows the SPR binding kinetics at 25° C. of various concentrations of vancomycin passing over surfaces of total isolated LPS from waaL+.

FIG. 11 shows the SPR binding kinetics at 25° C. of various concentrations of vancomycin passing over surfaces of total isolated LPS from waaL15.

FIG. 12 shows the reference subtracted SPR binding kinetics at 25° C.

FIG. 13 shows fluorescence microscopy images of waaL+ and waall15.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure generally relates to the genetic engineering of bacteria. More particularly, the present disclosure relates to genetic engineering of a gram-negative bacteria expressing a modified LPS molecule, and methods for making and using the molecule.

While the present disclosure is susceptible to various modifications and alternative forms, specific example embodiments are herein described in more detail. It should be understood, however, that the description of specific example embodiments is not intended to limit the invention to the particular forms disclosed. The features and advantages of the present invention will be apparent to those skilled in the art. While numerous changes may be made by those skilled in the art, such changes are within the spirit of the invention.

A recently described lptE mutation (lptE613) causes defective LPS transport and leads to increased antibiotic sensitivity (Malojc̆ié et al., 2014). In certain aspects of the invention, an isolated vancomycin-resistant strain of E. coli carrying a F332S substitution in the O-antigen ligase gene (waaL) and capable of restoring vancomycin resistance was isolated and characterized (See FIG. 1).

One embodiment of this invention increases vancomycin resistance in strains carrying bamB or bamE null mutations that disrupt the OM barrier by causing defects in β-barrel protein assembly (See FIG. 1). Certain embodiments of the invention also increase vancomycin-resistance across different strains, including the wild-type strain (See FIG. 1).

The domesticated E. coli K-12 does not produce the normal substrate (O—Ag) of waaL (Liu and Reeves, 1994) and a waaL deletion does not suppress vancomycin sensitivity, indicating that waaL15 is a gain of function mutation. Thus, certain aspects of the embodied invention must have an altered activity. Silver-staining of isolated LPS confirmed that waaL15 modifies LPS with additional sugars to produce one embodiment of this invention, a novel glycoform (LPS* herein), detected as a higher molecular weight band that is absent in waaL+ (See FIG. 3).

WaaL can use two minor saccharide substrates to modify LPS in E. coli K-12: enterobacterial common-antigen (ECA) and colanic acid (CA). ECA-modified LPS is a minor constituent of the OM (Schmidt et al., 1976; Meredith et al., 2007). Production of CA is regulated by the Rcs phospho-relay stress response system, and CA-modified LPS (called ‘M-LPS’) is only detectable during severe envelope stress (Meredith et al., 2007). LPS silver-staining revealed that LPS* remained detectable following inactivation of biosynthesis of ECA (rff), CA (cpsG), or both these polysaccharides (rff cpsG) (See FIG. 3). Increasing the amounts of a competing substrate by introducing the rcsC137 mutation to activate expression of the genes for CA biosynthesis (Gottesman et al., 1985), lowered LPS* abundance at the expense of increased M-LPS (See FIG. 4). The decrease in LPS* correlated with a significant reduction in vancomycin-resistance, indicating that LPS* molecules directly mediate the resistance (FIG. 5). WaaL15 is able to use a new substrate and thereby generate a previously uncharacterized LPS glycoform that provides a specific mechanism for vancomycin resistance.

All native WaaL substrates contain carbohydrates linked to a common undecaprenyl (Und) lipid carrier. PG biosynthesis involves a disaccharide pentapeptide (DPP) linked to the same Und carrier, a molecule called lipid II (See FIG. 6). Isolated LPS* was treated with the muralytic enzyme mutanolysin (See FIGS. 6 and 7). Digestion of purified LPS*, but not LPS, liberated near-stoichiometric quantities of fragments that were identified by mass spectrometry as DPP or derivatives with a tetrapeptide stem (See FIG. 8). There was no evidence for cross-linked products suggesting that lipid II was the source of the LPS* glycosylation.

There are several carboxypeptidases in the periplasm that remove the terminal D-Alanine (D-Ala) from DPP to produce the tetrapeptide derivative. Indeed, E. coli PG contains negligible amounts of pentapeptide stems. FIG. 8 shows that, in at least one instance, about 50% of the LPS* is sequestered before it can be attacked by one of these carboxypeptidases. It is expected that sequestration occurs because the molecule is transported from the periplasm to the cell surface.

Peptide stems from adjacent peptidoglycan strands in the cell wall are cross-linked via transpeptidation between the penultimate D-Ala on one stem and a meso-diaminopimelic acid(m-DAP) residue on a nearby stem (Vollmer et al., 2008). Extensive cross-linking produces a rigid macromolecular meshwork that is vital to cell wall function. Vancomycin binds and sequesters the terminal D-Ala-D-Ala residues of a pentapeptide stem in order to inhibit transpeptidation (Perkins, 1969). Since LPS* was the product of DPP ligation onto LPS, this modified glycoform should contain vancomycin binding sites.

Several vancomycin-resistance mechanisms exist in Gram-positive bacteria, including: alterations in peptidoglycan metabolism can produce thicker cell walls (Cui et al., 2003); and transpeptidation can be reduced to leave more free D-Ala-D-Ala residues within the established cell wall structure (Sieradzki and Tomasz, 1997). In one aspect of the invention, it has been shown that the waaL15 mechanism is comparable since it also increases the number of free D-Ala-D-Ala targets that can tie up vancomycin. Moreover, by displaying D-Ala-D-Ala at the cell surface the waaL15 mutation titrates vancomycin away from the true drug target, in an altogether different cellular compartment. Therefore, certain embodiments of the invention confer resistance by acting as a molecular decoy for vancomycin.

It should be understood by those skilled in the art that in certain other embodiments, the present disclosure may provide improved delivery of vaccines or improved vaccine adjuvants derived from the LPS* molecule of the present invention.

The biosynthesis of LPS* is remarkable. Lipid II in E. coli is extremely scarce, its steady-state abundance is thought to be only 1,000-2,000 molecules per cell (van Heijenoort et al., 1992). Insertion of new PG is thought to occur via large multiprotein morphogenic complexes: the elongasome and the divisome, responsible for PG synthesis along the lateral cell body and at the septum, respectively. In order to overcome the scarcity of lipid II and limit its diffusion away from sites of PG growth, both complexes are suggested to include at least some of the lipid II biosynthetic enzymes, and the presumed flippases that deliver lipid II from the site of synthesis in the cytoplasm to the site of cell wall assembly in the periplasm (Szwedziak and Lowe, 2013). In this model, the substrate for PG synthesis would be isolated physically from the LPS assembly pathway. LPS is inserted into the OM of each cell at a rate exceeding 70,000 molecules per minute (Lima et al., 2013). It is estimated that approximately one-third of LPS is modified by WaaL15 with lipid II-sourced DPP. Clearly, WaaL15 has ready access to lipid II and this is inconsistent with a model of diffusion-limited lipid II sequestered at the elongasome or divisome complexes. Recent evidence also points to wider lipid II availability (Lee et al., 2014; Sham et al., 2014). The re-charging of the lipid carrier with new DPP must also be extremely efficient to maintain such a robust pool of PG precursor.

WaaL15 drains the available lipid II pool with no apparent detriment to cell wall integrity. Lipid II limitation can be revealed by synthetic genetic interactions in a strain lacking the elongasome (Paradis-Bleau et al., 2014), but it is not the recharging of lipid II that is limiting, rather it is the biosynthesis of DPP. Table 1 lists some synthetic interactions between waaL15 and mutations affecting the elongasome due to limited lipid II availability.

TABLE 1 Relevant Genes* Cotransduction Donor Recipient Selected Allele Gene Frequency yhfT3084::Tn10 mrcA::kan waaL⁺ yhfT-3084::Tn10 mrcA::kan 85% yhfT3084::Tn10 mrcA::kan waaL15 yhfT-3084::Tn10 mrcA::kan 89% sfsB203::Tn10 lpoA::kan waaL⁺ sfsB203::Tn10 lpoA::kan 29% sfsB203::Tn10 lpoA::kan waaL15 sfsB203::Tn10 lpoA::kan 28% zad-220::Tn10 mrcB::kan waaL⁺ zad-220::Tn10 mrcB::kan 72% zad-220::Tn10 mrcB::kan waaL15 zad-220::Tn10 mrcB::kan 13% zce-726::Tn10 lpoB::kan waaL⁺ zce-726::Tn10 lpoB::kan 77% zce-726::Tn10 lpoB::kan waaL15 zce-726::Tn10 lpoB::kan 5% pMurA† zad-220::Tn10 mrcB::kan waaL⁺ zad-220::Tn10 mrcB::kan 79% zad-220::Tn10 mrcB::kan waaL15 zad-220::Tn10 mrcB::kan 77% zce-726::Tn10 lpoB::kan waaL⁺ zce-726::Tn10 lpoB::kan 75% zce-726::Tn10 lpoB::kan waaL15 zce-726::Tn10 lpoB::kan 70% *mrcA encodes PBP1A which functions with LpoA in the divisome; mrcB encodes PBP1B which functions with LpoB in the elongasome. †Expression of murA was induced by supplementing growth media with 100 μM IPTG.

In many bacteria, LPS is decorated with highly variable O-Ags that are linear polymers of repeating units of 3-6 monosaccharides (Kalynych et al., 2014). In E. coli the multitude of different O-Ags initiate with GlcNAc, ECA also initiates with GlcNAc. In E. coli K-12 when colonic acid is overproduced M-LPS is made from an initiating Glc residue. The F332S mutation broadens substrate specificity of the WaaL glycosyltransferase allowing it to efficiently accept a significantly more bulky initiating MurNAc with an attached oligopeptide stem. The only other glycosyltransferase that is known to use lipid II as a substrate is Pg1L from Neisseria and the use required overproduction of the enzyme in E. coli (Faridmoayer et al., 2008). It is also remarkable that no OM biogenesis defect in strains carrying waaL15 is detected, demonstrating that the Lpt system is fully competent for the transport and assembly of LPS* despite the addition of both unnatural sugars and peptide stems. Both LPS and PG are pathogen-associated molecular patterns (PAMPs) that potently activate innate immune responses via distinct pathways, and it seems sensible for Gram-negative bacteria to keep these entities separated. It is expected that the F332S substitution has inactivated an exclusion mechanism that prevents WaaL from utilizing the lipid II pool.

In certain embodiments of the invention, the present disclosure provides for bacteria modified with the waaL15 mutation, or a bacterium modified to express LPS*. During production of LPS*, the Escherichia coli waaL15 mutant bacteria typically produce both native LPS and the LPS* glycoform. Consequently, established “total LPS extraction” methods that have been performed on cultures of these bacteria yield a mixture of LPS and LPS*. While this may be sufficient for some purposes, it is expected that other purification methods, or a combination of methods, may provide improved isolation and purification of the LPS* component Other methods beyond “total LPS extraction” methods envisioned as part of this method include, but are not limited to, size-based chromatography that exploits LPS*'s increased size and altered chemical composition compared to LPS, or affinity-based methods that exploit the specific binding of LPS* to vancomycin.

The use of LPS as an adjuvant is precluded by strong endotoxicity. LPS derivates isolated following acid and base hydrolysis have significantly reduced endotoxicity but remain immunostimulatory. One such LPS derivative is 3-O-deacyl-4′-monophosphoryl lipid A (MPL, GSK) which is part of the adjuvant formulation ASO4 used in the Cervarix™ human papillomavirus vaccine (GSK). LPS* molecules are likely sensitive to acid and base hydrolysis. It is known in the art that strains of E. coli may be engineered to produce LPS derivatives without the need a harsh chemical treatment that would likely be incompatible with LPS*. It is therefore expected that introducing the waaL15 mutation into LPS derivative producing strains, such as those producing 3-O-deacyl-4′-monophosphoryl lipid A, will produce a detoxified LPS* derivative that retains at least some of the immunogenic properties of LPS*.

Certain embodiments of the invention provide for producing a modified lipopolysaccharide molecule that enables the molecule to activate at least some of the immune signaling receptors and pathways of traditional LPS and PG, including TLR4, MD2, NOD1, and NOD2 receptors, and TRIF/TRAM pathways. It is expected that applying LPS* treatment to human TLR4/MD2, NOD1, and NOD2 reporter cell lines will confirm signaling through this receptor and downstream pathway, and that LPS*-treated human cell lines will show activation via the TRIF/TRAM pathway using transcriptomic analysis.

To facilitate a better understanding of the present invention, the following examples of certain aspects of some embodiments are given. In no way should the following examples be read to limit, or define, the entire scope of the invention.

EXAMPLES

Construction of Mutant Strains

Strains and plasmids used in this study are listed in Table 2 and Table 3, respectively. Strains were grown in lysogeny broth (L B, Miller) or M63 minimal medium under aeration at 37° C. unless otherwise noted. When appropriate, media were supplemented with kanamycin (Kan, 25 μg/ml), ampicillin (Amp, 25-125 μg/ml), tetracycline (Tet, 20 μg/ml), chloramphenicol (Cam, 20 μg/ml), vancomycin (Vanc, 65-260 μg/ml) and arabinose (Ara, 0.2% v/v).

Kanamycin deletion-insertion mutations of bamE, cpsG, mrcA, mrcB, lpoA and lpoB were obtained from the Keio collection (Baba et al., 2006). ECA null rff::Tn10-66 allele was obtained from strain 21566 (Meier-Dieter et al., 1990). The ompC::Tn5 rcsC137 was obtained from strain SG20803 (Brill et at, 1988). Mutant alleles were introduced by P lvir transduction.

TABLE 2 Strain Relevant Genotype Reference MC4100 F⁻ araD139 l⁻ (arg-lac)U169 rpsL150 relA1 (Casadaban, 1976) flbB5301 deoC1 ptsF25 thi NR754 MC4100 Ara⁺ (Button et al., 2007) CAG12025 F⁻ araD139 l⁻ rph-1 zad-220::Tn10 (Singer et al., 1989) CAG12072 F⁻ araD139 l⁻ rph-1 sfsB203::Tn10 (Singer et al., 1989) CAG12078 F⁻ araD139 l⁻ rph-1 zce-726::Tn10 (Singer et al., 1989) CAG18456 F⁻ araD139 l⁻ rph-1 yhfT3084::Tn10 (Singer et al., 1989) MG617 NR754 ΔlptE2::kan/plptE⁺ (Maloj{hacek over (c)}ić et al., 2014) MG1029 NR754 ΔlptE2::kan/plptE613 (Maloj{hacek over (c)}ić et al., 2014) MG1088 NR754 ΔlptE2::kan waaL15/plptE613 This study MG1167 NR754 ΔlptE2 waaL15/plptE613 This study MG1180 MG1167 ΔcpsG::kan This study MG1181 MG1210 ΔbamE::kan This study MG1182 MG1211 ΔbamE::kan This study MG1196 MG1210 bamB::kan This study MG1197 MG1211 bamB::kan This study MG1210 NR754 waaL⁺ tdh::Tn10 This study MG1211 NR754 waaL15 tdh::Tn10 This study MG1214 MG1167 ΔcpsG::kan rff::Tn10 This study MG1234 MG1167 rff:Tn10-66 This study MG1378 MG1210 ompC::Tn5::kan rcsC137 This study MG1379 MG1211 ompC::Tn5 rcsC137 This study MG1642 NR754 waaL⁺ This study MG1643 NR754 waaL15 This study MG1635 CAG12025 ΔmrcB::kan This study MG1636 CAG18456 ΔmrcA::kan This study MG1671 CAG12072 ΔlpoA::kan This study MG1672 CAG12078 ΔlpoB::kan This study

TABLE 3 Plasmid Description Reference plptE lptE cloned into pBAD18, Amp^(R) (Wu et al., 2006) pMurA ASKA plasmid with cloned murA, Cam^(R) (Kitagawa et al., 2006)

Isolation and Identification of waaL15

Spontaneous suppressor mutants of strain MG1029 capable of growing on LB plates supplemented with vancomycin (140 μg/ml) were isolated; one such mutant strain was MG1088. The mutation locus conferring vancomycin-resistance in MG1088 was identified by linkage mapping using a library of random mini-Tn10 insertions (Kleckner et al., 1991). In this way, the tdh::Tn10 allele was found to be approximately 70% linked to the suppressor mutation waaL15. The F332S mutation was then identified by PCR amplification and sequencing of the waaL locus. The waaL15 mutation was moved into the NR754 wild-type strain by linkage with tdh::Tn10. In order to generate the unmarked waaL15 strain (MG1643) and its wild-type control (MG1642), the tdh::Tn10 mutation was removed from strains MG1210 and MG1211 by first introducing a linked ΔcysE::kan mutation (Baba et al., 2006), selecting for Kan^(R) and screening for Tets transductants that were Vanc^(R) (waaL15) or Vanc^(s) (waaL±). The AcysE::kan mutation was then replaced with cysE⁺ by transduction, selection on M63 minimal medium, and screening of Vanc^(R)/Vanc^(S).

Assessment of Genetic Linkage by Co-Transduction

The genetic interaction of PG synthase mutants with waaL15 was assessed as follows. Kan^(R)-marked null alleles of lpoA, lpoB, mrcA and mrcB were introduced by P1vir transduction into CAG strains that carry a Tn10 insertion in a nearby locus (see Table 1). Kan^(R) Tet^(R) transductants were isolated and used to generate Plvir lysates. These Plvir were used to transduce waaL⁺ (MG1642) or waaL15 (MG1643) strains, selecting for the Tn10 marker. The frequency with which the Kan^(R)-marked lpo and mrc alleles were co-transduced (genetically linked) was determined by replica plating on LB+Kan. Linkage was assessed in a total of 300 transductants from 3 independent experiments. A decrease in the cotransduction frequency in waaL15 strains relative to waaL±indicates a synthetic interaction between waaL15 and the Kan^(R)-marked allele. The synthetic interaction between waaL15 and mrcB/lpoB null alleles was relieved in strains carrying pMurA when expression of the cloned murA gene (encoding the enzyme responsible for the first committed step in DPP biosynthesis) was induced with 100 μM isopropyl β-D-1-thiogalactopyranoside (IPTG). Overexpression of murA increases the cellular pool of UDP-MurNAc-pentapeptide and consequently also increases the pool of lipid II.

Analysis of LPS by SDS-PAGE and Silver Staining

A total to 1×10⁹ cells from liquid culture were taken, pelleted and resuspended 0.05 ml of ‘LPS Sample Buffer’ (0.66 M Tris pH 7.6, 2% v/v sodium dodecyl sulfate [SDS], 10% v/vglycerol, 4% v/v 6-mercaptoethanol, 0.1% w/v bromophenol blue). Samples were boiled for 10 min and allowed to cool to room temperature. 10 μl of Proteinase K (2.5 mg/ml, in LPS SampleBuffer) was added and samples were incubated at 56° C. for 16 h. LPS samples were then resolved by SDS-PAGE and silver stained as described previously (Tsai and Frasch, 1981). By quantifying band density using ImageJ, it was determined that LPS* constituted 29 ±1% of the total LPS in waaL15 samples.

Antibiotic Disc Diffusion Assay

3 ml of molten LB Top agar (0.75% agar) was inoculated with 0.1 ml of overnight culture. The mixture was poured onto a LB agar plate (1.5% agar,) and allowed to set. Antibiotic discs (BD Sensi-Disc) were placed on the Top agar overlay and plates were incubated overnight at 37° C. The ‘zone of growth inhibition’ was measured across the antibiotic disc.

Fluorescence Microscopy

Overnight cultures were sub-cultured at 1:100 into fresh LB broth and grown for 1.5 h. Al ml aliquot was taken, pelleted and was twice washed with 1 ml M63 medium. Cells were resuspended in 0.1 ml of M63 broth containing 1 μg/ml of vancomycin-BODIPY-FL (LifeTechnologies, V-34850). Cells were incubated at room temperature for 10 min and then washed twice with 1 ml M63 broth. Cells were then resuspended in 0.03 ml of M63 broth, and approximately 2 ml was spotted onto an M63-agarose pad. Cells were immediately visualized on a Nikon Eclipse 90i microscope with a Nikon Plan Apo 1.4/100×Oil Ph3 phase objective.

LPS Purification

E. coli MG1210 and MG1211 were each grown in 4×1.5 l LB medium shaking at 37° C. overnight to stationary phase. The cells were harvested by centrifugation for 15 min at 5,000× g, 4° C. and washed with water (700 ml) and ethanol (40 ml) once, then twice with acetone (40 ml). After drying the cell pellet in a desiccator overnight in vacuo, PCP (Phenol-Chloroform-petroleum ether) method was used for rough LPS extraction (Galanos et al., 1969).

PG Purification

E. coli MG1210 and MG1211 were each grown in 500 ml LB medium shaking at 37° C. to stationary phase (6 h). The cell wall was isolated from the culture as described by Glauner etal., (1988) and Uehara et al., (2009), with modifications described below. The cells were resuspended in 20 ml phosphate buffered saline (PB, pH =7.4) and boiled for 30 min in 80 ml 5% SDS. After the samples cooled, they were pelleted (14,000 rpm, 25° C., 1 h) and washed six times by pelleting (14,000 rpm, 25° C., 1 h) from 50 ml water aliquots to remove the SDS. The samples were resuspended in 1 ml PBS, treated with a-amidase (100 μl, 2 mg/ml stock in 50% glycerol, Sigma A-6380) and incubated at 37° C. with shaking for 2 h. To cleave proteins attached to the cell wall, a-chymotrypsin (100 μl, 3 mg/mL in 50% glycerol, Sigma C3142) was added, and the samples were incubated at 37° C. with shaking overnight. An additional aliquot of α-chymotrypsin (100 μl) was added, and the samples were digested for an additional 4 h. To remove the proteins, SDS was added to a final concentration of 1%, and the samples were incubated at 95° C. for 1 h. After cooling, the samples were again pelleted (14,000 rpm, 25° C., 1h) and washed with water repeatedly (4×25 ml) to remove the SDS. The final peptidoglycan (PG) samples were resuspended in 500 μL 0.02% azide and stored at 4° C.

Mutanolysin Digestion and Analysis

The PG composition was analyzed by LC/MS as previously described (Lebar et a/.,2013). The method was also used to analyze LPS samples. The glycosyl hydrolase mutanolysin liberated DPP and disaccharide tetrapeptide from LPS*. Aliquots (40 μl) of PG (from MG1210and MG1211) and LPS (from MG1210 and MG1211) were incubated with mutanolysin (10 U, 2.5 μl, 4000 U/ml, Sigma M9901, stored at −20° C. in 50 mM TES, pH 7.0, 1 mM MgCl2, 10% glycerol) in 50 mM sodium phosphate buffer (pH 6.0, 100 pl total volume) at 37° C. with shaking overnight. Another aliquot of mutanolysin (10 U, 2.5 pl) was added, and the mixture was incubated at 37° C. with shaking for 3 h. Insoluble particles were separated by centrifugation (16,000× g). The supernatant, containing soluble fragments, was treated with sodium borohydride (10 mg/ml in water, 100 μL) at room temperature for 30 min. Phosphoric acid (20%,12 μl) was then added to adjust pH to ˜4. When bubbling ceased, the samples were lyophilized and re-dissolved in 25 pl water, which was analyzed on LC/MS. LC/MS analysis was conducted with ESI-MS operating in positive mode. The instrument was equipped with a Waters Symmetry Shield RP18 column (5 μm, 3.9×150 mm) with matching column guard. The fragments were separated using the following method: 0.5 ml/min H₂O (0.1% formic acid) for 5 min followed by a gradient of 0% ACN (0.1% formic acid)/H₂O (0.1% formic acid) to 20% ACN (0.1% formic acid)/H₂O (0.1% formic acid) over 40 min.

Surface Plasmon Resonance Analysis

Purified LPS (0.5 mg/ml) from strains MG1210 or MG1211 were extruded in 20 mMTris/HCl pH 8, 150 mM NaCl and immobilized on poly-L-lysine coated CM3 Biacore chips on the active and reference channel, respectively (Malojeie et al., 2014). All experiments were performed using a Biacore X100 instrument at 25° C. at a flow rate of 10 μl/min with 20 mMTris/HCl pH 8, 150 mM NaCl buffer. Different concentrations of vancomycin were injected for 400 s and dissociation was recorded for another 500 s to return to baseline. No binding was observed to the reference channel. The equilibrium signal in the difference channel was fitted to f=Bmax*abs(x)/(K_(d)+abs(x)) with R²=0.88. Standard deviation was measured for 0.6 μM and 1.2 μM vancomycin in triplicate and did not exceed 1 RU.

Assessment of Vancomycin Binding Ability

The ability of purified LPS* to bind vancomycin in vitro was assessed. LPS* was immobilized on a carboxymethylated dextran (CM3) chip and surface plasmon resonance was used to monitor interactions with differing concentrations of vancomycin. The specific binding of vancomycin to LPS* was measured and a K_(d)=0.48±0.08 μM was obtained (See FIGS. 9-12), which is comparable to a reported K_(d) for vancomycin-lipid II interactions invesicles (Al-Kaddah et al., 2010). Clearly, LPS* molecules include high affinity binding sites for vancomycin. The ability of LPS* to directly bind vancomycin suggested a possible resistance mechanism, namely that vancomycin is titrated outside the cell. To test this hypothesis, weperformed live cell microscopy using a fluorescent vancomycin-BODIPY. A wild-type strain background with an intact OM that prevents the influx of vancomycin was used, to avoid labeling intracellular sites of PG synthesis. Indeed, waaL⁻ cells could not be fluorescently labeled (See FIG. 13). On the other hand, circumferential labeling of waaL15 bacteria was readily detected, confirming the presence of accessible D-Ala-D-Ala residues at the cell surface (See FIG. 13).

Comparative Analysis of LPS* and LPS

Traditional adjuvants (e.g. aluminum salts) are potently immunogenic but produce a biased immune response. Specifically, these adjuvants are poor at eliciting a TH1 response to vaccine components. Activation of TH1 responses is important for generating protective antibacterial and antiviral immunity against many pathogens. It is established that the adjuvant effect of LPS produces a TH1-biased immunity. It is also established that LPS-stimulated immune signaling pathways are synergistically activated when provided with additional stimulation with NOD ligands (PG components). By utilizing reporter human cell lines to quantify the strength of immune activation, including activation via TLR4/MD2, NOD1 and NOD2 receptors, the LPS* immune response can be compared to LPS via transcriptomic analysis. The production of immune effector molecules (including cytokines and chemokines) can be characterized using commercially available protein detection assays. It is expected that LPS* will provide more robust immune activation, or result in a distinct profile of immune responses (e.g. biased to TH1-type immunity) and/or distinct production of effector molecules (including cytokines and chemokines) in comparison to LPS, owing to activation of TLR4 and NOD1/2 signaling.

Assessing the adjuvant properties of LPS* and derivative molecules

The ability of LPS* and its derivatives to elicit protective immunity can be assessed by using these molecules as part of an adjuvant formulation in vaccinations or using model antigens. In one example, mice can be immunized against the ovalbumin antigen by vaccination with formulations where the adjuvant is either an LPS* derivative, or an LPS derivative or alum. The immune response of these mice to vaccinations can be assessed and compared. In another example, the ability of LPS* to elicit protective immunity can be assessed using model pathogens. Mice can be immunized against pathogen antigens by vaccinations formulated with LPS*-based, LPS-based, or alum-based adjuvants. Mice can then be challenged with the pathogen and survival will be recorded and compared to LPS. It is expected that LPS* and its derivatives will provide more robust immunity or result in an altered immunity that improves the efficacy of immunization, compared to LPS and its derivatives. 

What is claimed is:
 1. A vaccine adjuvant comprising at least one of a lipopolysaccharide isolated from a mutant O-antigen ligase or lipopolysaccharide derivative isolated from the mutant O-antigen ligase, the mutant O-antigen ligase comprising either an isolated protein that has the amino acid sequence SEQ ID NO: 1, or an isolated protein having at least 90% sequence identity to SEQ ID NO: 2 and having an amino acid substitution of phenylalanine to serine at the phenylalanine homologous to position 332 of SEQ ID NO: 2, wherein the isolated protein has at least one of 0-antigen ligase activity or the activity to ligate lipid A to disaccharide pentapeptide (DPP).
 2. A vaccine adjuvant comprising a lipopolysaccharide derivative molecule prepared by the process comprising the steps of: providing an E. coli strain adapted to express an LPS derivative molecule; modifying the E. coli strain by creating a mutant 0-antigen ligase selected from the group consisting of: a mutant O-antigen ligase comprising an isolated protein that has the amino acid sequence SEQ ID NO: 1, and a mutant O-antigen ligase comprising an isolated protein having at least 90% sequence identity to SEQ ID NO: 2 and having an amino acid substitution of phenylalanine to serine at the phenylalanine homologous to position 332 of SEQ ID NO: 2, wherein the protein has at least one of 0-antigen ligase activity or the activity to ligate lipid A to disaccharide pentapeptide (DPP); providing a growth media for the modified E. coli strain; and allowing the modified E. coli strain to produce an LPS* derivative molecule, wherein the LPS* derivative molecule includes at least one non-native sugar not present in an LPS molecule it derives from. 